飯間 信 教授/ IIMA Makoto Professor


We study bio-fluid mechanics and related problems such as flight and swimming of animals, collective behaviors of microorganisms, and transportation inside body, by using mathematical analysis. Our aim is to extract essential behavior of biological activity, movements and functions in terms of mathematics for future applications.

keywords:fluid mechanics, biofluid, swimming, flight, collective behavior, mathematical structure

  1. Emergence of a Euglena bioconvection spot controlled by non-uniform light, Front. Ecol. Evol. 11:1132956(2023).
  2. Phase reduction technique on a target region, Phys Rev E, 103: 053303(2021)
  3. Active lift inversion process of heaving wing in uniform flow by temporal change of wing kinematics, Phys Rev E, 99: 043110(2019)
泉 俊輔 教授/ IZUMI Syunsuke Professor


The ionization method called MALDI can acquire “mass information” and “position information” at the same time, but by combining this with the MALDI method that does not use a matrix, we would like to start the development of “micro natural product chemistry.”

keywords:MALDI, mass information, position information

  1. Mass spectrometric characterization of histone H3 Isolated from in-Vitro reconstituted and acetylated nucleosome core particle/Mass
  2. 3-Hydroxy-4-nitrobenzoic Acid as a MALDI Matrix for In-Source Decay/ Analytical Chemistry / 2016
  3. Alkylated Trihydroxyacetophenone as a MALDI Matrix for Hydrophobic Peptides/ Analytical Chemistry/ 2013
坂本 敦 教授/ SAKAMOTO Atsushi Professor


My research interests lie in plant science, primarily elucidating molecular mechanisms of how plants respond to and survive in changing environments. Applied research is also conducted to exploit the capabilities of plants, including microalgae, for better performance under stress and towards the practical production of useful substances such as biofuels.

keywords:plant molecular physiology, plant hormone, plant metabolite, stress response, stress tolerance, biotechnology

  1. Dynamics of the leaf endoplasmic reticulum modulate ß-glucosidase-mediated stress-activated ABA production from its glucosyl ester, J
    Exp Bot, 71: 2058-2071(2020)
  2. Allantoin, a stress-related purine metabolite, can activate jasmonate signaling in a MYC2-regulated and abscisic acid-dependent manner,
    J Exp Bot, 67: 2519-2532(2016)
  3. The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism, Plant Cell
    Environ, 37: 1022-1036(2014)
楯 真一 教授/ TATE Shinichi Professor


My research focus is on the structure and function relations of intrinsically disordered proteins(IDPs) that constitute about 50% of human proteins with combinatorial use of theoretical and experimental approaches including NMR, molecular dynamics simulation, biochemistry, and cell biology. Students with a physics diploma are very welcome.

keywords:biophysics, structural biology, protein, IDP

  1. Ultrasensitive Change in Nucleosome Binding by Multiple Phosphorylations to the Intrinsically Disordered Region of the Histone Chaperone FACT/J.Mol.Biol./2020
  2. Non-RVD mutations that enhance the dynamics of the TAL repeat array along the superhelical axis improve TALEN genome editing efficacy/Sci. Rep./2016
  3. Allosteric breakage of the hydrogen bond within the dual-histidine motif in the active site of human Pin1 PPIase/Biochemistry/2015
中田 聡 教授/ NAKATA Satoshi Professor


Rhythm and pattern observed in living organisms and nature are called “self-organization. ”Artificial experimental systems are developed to physicochemically elucidate the mechanism of self-organziation. Characteristic features of motion, such as collective motion and synchronized sailing, and oscillatory motion of self-propelled objects and chemical oscillation are examined.

keywords:self-organization, oscillation, pattern formation, synchronization

  1. Evolution of self-propelled objects – From the viewpoint of nonlinear science, Chem. A Euro. J., 2018.
  2. Self-propelled motion of a coumarin disk characteristically changed in couple with hydrolysis on an aqueous phase, J. Phys. Chem. B,2019.
  3. Chemical wave propagation in the Belousov-Zhabotinsky reaction controlled by electrical potential, J. Phys. Chem. A, 2019.
藤本 仰一 教授/ FUJIMOTO Koichi Professor


Theoretical study (mathematical modeling and data analysis) of evolving multi-level dynamics (gene expression,shape, and behaviors) in plants, animals, and microbes.

keywords:theoretical biology, complex systems, biophysics, evolution, diversity, multi-scales

  1. Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis. Current Biology 33: 886-898.e8(2023)
  2. A design principle for floral organ number and arrangement in flowers with bilateral symmetry. Development 147:20200204(2020)
  3. Competition for Space Is Controlled by Apoptosis-Induced Change of Local Epithelial Topology. Current biology 28: 2115-2128(2018)
坊農 秀雅 教授/ BONO Hidemasa Professor


Toward data-driven genome breeding (digital breeding), we are developing data analysis infrastructure technology essential for genome editing, focusing on gene function analysis using bioinformatics called BioDX.

keywords:BioDX, bioinformatics, genome editing, transcriptome analysis, functional annotation, public database, open source software, hypoxia, oxidative stress, meta-analysis

  1. A highly contiguous genome assembly of red perilla(Perilla frutescens) domesticated in Japan. DNA Research, 30:dsac044(2023)
  2. Systematic functional annotation workflow for insects. Insects, 13:586(2022)
  3. Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence set. Life Science Alliance, 6: e202201518
本田 直樹 教授/ HONDA Naoki Professor


To understand the mechanisms behind dynamic and complex biological phenomena, we are combining mathematical modeling and machine learning for decoding the governing rules or equations that govern biological systems.

keywords:data-driven biology, mathematical modeling, machine learning

  1. Decoding reward–curiosity coflict in decision-making from irrational behaviors. Nature Computational Science 3, 418–432(2023)
  2. Stem cell homeostasis regulated by hierarchy and neutral competition. Communication Biology 5, 1268(2022)
  3. Model-based prediction of spatial gene expression via generative linear mapping. Nature Communications 12: 3731(2021)
山本 卓 教授/ YAMAMOTO Takashi Professor


We are developing genome editing technologies that can be used in various organisms and trying their use in various fields.

keywords:genome editing, developmental biology

  1. Biased genome editing using the local accumulation of DSB repair molecules system, NATURE COMMUNICATIONS, 9:3270(2018)
  2. Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells, CELL, 78:491-506.e28(2019)
  3. Zinc-finger nuclease-mediated targeted insertion of reporter genes for quantitative imaging of gene expression in sea urchin embryos,PNAS, 109:10915-20(2012)
粟津 暁紀 准教授/ AWAZU Akinori Associate Professor


We progress theory-experimant hybrid studies for  i)structural dynamics of biomolecular populations, ii)genome dynamics and gene regulation, iii) development and morphogenesis of multi-cellular organisms.

keywords:Mathematical model, Biological and medical data analysis, Experiment for molecular and developmental biology

  1. Partial exogastrulation due to apical-basal polarity of F-actin distribution disruption in sea urchin embryo by omeprazole. Genes to Cells 1-17(2022)
  2. Epigenetic-structural changes in X chromosomes promote Xic pairing during early differentiation of mouse embryonic stem cells. Biophys. and Physicobiol. 19, e190018(2022)
  3. Formation of Small-World Network Containing Module Networks in Globally and Locally Coupled Map System with Changes in Global Connection with Time Delay Effects. J. Phys. Soc. Jpn. 92, 034801(2023)
大西 勇 准教授/ OHNISHI Isamu Associate Professor


With nonlinear partial differential nonlinear equations as main target, analysis of nonlinear phenomena as mathematical analysis in a broad sense, as pure mathematical science.

keywords:system of nonlinear partial d ifferential equations, l ife and/or biological nonlinear phenomena, mathematical analysis in a broad sense

  1. “Standard model of a binary digit of memory with multiple covalent modifications in a cell”, J. of pure and applied math., 2(1), p1 – 11(2018)
  2. “Bifurcation analysis to Lugiato-Lefever equation in one space dimension”, Physica D, 239,( 2010) 2066 -- 2083.
  3. “A mathematical study of the one dimensional Keller and Rubinow model for Liesegang bands”, J. Stat Phys( 2009) Vol. 135: 107–132
片柳 克夫 准教授/ KATAYANAGI Katsuo Associate Professor


Structure and function analysis of protein by X-ray crystallography. Target proteins are DNA-repair enzyme; toxin proteins from Staphylococcus aureus; lectin from algae; proteins relating to cancer and Parkinson’s disease; proteins from plant; glucokinase, and so on. Molecular evolution of protein is also analyzed from X-ray structure of artificial proteins.

keywords:protein, crystallography, structural biology, chemistry, physics, data science, synchrotron radiation, pharmacy

  1. Three-dimensional structure of ribonuclease H from E. coli./Nature 347, 306–309/1990
  2. X-ray structure of T4 endonuclease V: An exision repair enzyme specific for a pyrimidine dimer./Science 256, 523-526/1992
  3. Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high resolution structures./Prot.
    Sci. 21, 383-395/2012
斉藤 稔 准教授/ SAITO Nen Associate Professor


The aim of our research group is to understand dynamic and complex biological phenomena from the perspective of biophysics and mathematical biology, and to elucidate the underlying mechanisms universal to various biological species through mathematical modeling, machine learning analysis, and large scale numerical computation.

keywords:biophysics, mathematical biology

  1. Three-dimensional morphodynamic simulations of macropinocytic cups. iScience 24(10) 1-22(2021)
  2. A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape. NPJ Syst. Biol. Appl. 9(1), 30. 1-12(2023)
  3. Theoretical analysis of discreteness-induced transition in autocatalytic reaction dynamics. Phys. Rev. E. 91, 022707 1-7(2015)
坂本 尚昭 准教授/ SAKAMOTO Naoaki Associate Professor


Using sea urchin development as a model, I aim to elucidate the molecular mechanisms for transcriptional regulation of morphogenetic genes, nuclear dynamics of gene, chromatin and chromosome during development, and insulator activity with molecular biology techniques and genome editing.

keywords:sea urchin development, transcription, nuclear dynamics

  1. Establishment of knockout adult sea urchins by using a CRISPR-Cas9 system. Dev Growth Differ 61:378-388.(2019)
  2. Dynamic changes in the interchromosomal interaction of early histone gene loci during development of sea urchin. J Cell Sci 130:4097-4107.(2017)
  3. Cilia play a role in breaking left–right symmetry of the sea urchin embryo. Genes Cells 21:568-578.(2016)
島田 裕士 准教授/ SHIMADA Hiroshi Associate Professor


We are studying the mechanisms to increase photosynthesis activity, which may contribute to the reduction of CO₂ as greenhouse gas, and countermeasures against the global food crisis. We have revealed several mechanisms of inhibition of photosynthetic protein oxidation and have succeeded in breeding plants with increased photosynthetic activity.

keywords:photosynthesis, Rubisco, redox, oxidative stress

  1. Overexpression of BUNDLE SHEATH DEFECTIVE 2 improves the efficiency of photosynthesis and growth in Arabidopsis.(2020) Plant J.102: 129-137.
  2. Arabidopsis BSD2 reveals a novel redox regulation of Rubisco physiology in vivo.(2020) Plant Signal. Behav. 15
  3. Overexpression of the protein disulfide isomerase AtCYO1 in chloroplasts slows dark- induced senescence in Arabidopsis.(2018) BMC Plant Biology 18: 1-9.
藤原 好恒 准教授/ FUJIWARA Yoshihisa Associate Professor


Research fields consist of(1) effect of steady high magnetic fields up to 200,000 gauss and(2) effect of magnetically regulated gravitational fields, especially microgravity and hypergravity, on photochemical reactions and biological phenomena of Aspergillus oryzae.

keywords:magneto-science, magnetic field, magnetically regulated gravitational field, microgravity, hypergravity, photochemical reation, Aspergillus oryzae

  1. Effect of High Magnetic Fields on the Reverse Electron Transfer Process in an α-Cyclodextrin Inclusion Complex of Phenothiazine-Viologen Chain-Linked Compound / Chem. Phys. Lett., 259, 361-367 / 1996.
  2. Effect of Horizontal Strong Static Magnetic Field on Swimming Behavior of Paramecium caudatum / Mol. Phys., 104, 1659-1666 / 2006.
  3. Effect of Hypergravity Created by Strong Magnetic Force on Orientation of Porphyrin Nanorods / J. Magn. Magn. Mater., 310, 2859-2861 / 2007.
芦田 嘉之 助教/ ASHIDA Yoshiyuki Assistant Professor
大前 英司 助教/OOMAE Eiji Assistant Professor


Since the internal and external hydrostatic pressures of deep-sea microorganisms are the same, their enzymes must work under high hydrostatic pressure and have some kind of pressure-adaptation mechanisms.Elucidation of such pressure-adaptation mechanisms of deep-sea enzymes can contribute to basic bioscience and industrial applications.

keywords:deep sea enzyme, high pressure, hydration, molecular adaptation, partial molar volume

  1. Functional, structural, and thermodynamic characteristics of enzymes from deep-sea microorganisms. Microbial Catalysts Volume 1: 325-343(2019).
  2. Stability, flexibility, and function of dihydrofolate reductases from Escherichia coli and deep-sea bacteria. Current Research in Microbiology:1-36(2018).
  3. Similar structural stabilities of 3-isopropylmalate dehydrogenases from the obligatory piezophilic bacterium Shewanella benthica strain DB21MT-2 and its atmospheric congener S. oneidensis strain MR-1. Biocim. Biophys. Acta 1866: 680-691(2018).
高橋 美佐 助教/ TAKAHASHI Misa Assistant Professor


Nitrogen dioxide is a trace component of the atmosphere, and is used to be known as a pollutant. I have found that nitrogen dioxide is a positive regulator for plants to nearly double their organ size and shoot biomass. I have been studying the molecular mechanism how nitrogen dioxide acts on plants.

keywords:nitrogen dioxide, nitrogen oxide, Plant, Arabidopsis, environment

  1. Dual selective nitration in Arabidopsis: Almost exclusive nitration of PsbO and PsbP, and highly susceptible nitration of four non-PSII proteins, including peroxiredoxin II E/Electrophoresis/2015
  2. Nitrogen dioxide regulates organ growth by controlling cell proliferation and enlargement in Arabidopsis/New Phytol/2014
  3. Atmospheric nitrogen dioxide gas is a plant-vitalization signal to increase plant size and the contents of cell constituents/New Phytol/2005


中坪(光永)敬子 助教/MITSUNAGA-NAKATSUBO Keiko Assistant Professor


To understand the morphological diversity and conservation of multicellular animals, I have been studying the regulatory mechanisms for morphogenesis during development using sea urchin, medaka and mouse. I am currently investigating the molecular environment, function and evolution of novel extracellular matrix, which is indispensable for constructing multicellular systems.

keywords:morphogenesis, development, extracellular matrix, cell differentiation

  1. Cell-surface arylsulfatase A and B on sinusoidal endothelial cells, hepatocytes, and Kupffer cells in mammalian livers. Med Mol Morphol 42:63-69.(2009)
  2. Sea urchin arylsulfatase, an extracellular matrix component, is involved in gastrulation during embryogenesis. Dev Genes Evol 219:281-288.(2009)
  3. Distributions of H+,K+-ATPase and Cl-,HCO3(-)-ATPase in micromere-derived cells of sea urchin embryos. Differentiation 35:190-196.(1987)
藤井 雅史 助教/ FUJII Masashi Assistant Professor


We aim to understand biological phenomena by using mathematical modeling and data analysis. Recently, we are focusing on the relationship among structure, movement and function of molecules, subcellular organelles and cells.

keywords:mathematical modeling, statistics, biophysics, systems biology, bioinformatics

  1. Logical design of oral glucose ingestion pattern minimizing blood glucose in humans/npj Syst. Biol. Appl. 5:31/2019
  2. Robustness against additional noise in cellular information transmission/Phys. Rev. E 100:042403/2019
  3. Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine/Biophys. J. 112:813/2017
松尾 宗征 助教/MATSUO Muneyuki Assistant Professor


Construct artificial life-like systems from the aspects of supramolecular chemistry and nonlinear science to approach universal answers to “Origins of Life” and “What is Life?”. Also try to apply characteristic features of life to industry.

keywords:supramolecular chemistry, nonlinear science, life-like systems, protocells, artificial cells, origins of life

  1. Proliferating Coacervate Droplets as the Missing link between Chemistry and Biology in the Origins of Life. Nature Commun 12(1): 5487 (2021)
  2. Evolution of Proliferative Model Protocells Highly Responsive to the Environment. Life 12(10):1635 (2022)
  3. Oscillatory Motion of an Organic Droplet Reflecting a Reaction Scheme. J Phys Chem Lett 14: 14546-14551 (2023)
安田 恭大 助教/ YASUDA Kyota Assistant Professor


My research interest is in the mechanisms of cell-polarization, and how they contribute to  biological events, including human disease.

keywords:cell polarity, biomolecular condensates, local translation, bio-imaging

  1. “The RNA-binding protein Fus directs translation of localized mRNAs in APC-RNP granules.” eLife, 2019
  2. “FUS inclusions disrupt RNA localization by sequestering kinesin-1 and inhibiting microtubule detyrosination.” J. C. Biol., 2017.
  3. “Translation regulation of protrusion-localized RNAs involves silencing and clustering after trasnport..” J. C. Biol., 2013.